Research workbench
Crystal structure of the neutralizing Fab fragment ABD1556 bound to the bmp type I receptor ia
Analyse Crystal structure of the neutralizing Fab fragment ABD1556 bound to the bmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NH7
- Type
- protein
- Length
- 2,038 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody fragment Fab ABD1556, heavy chain; Antibody fragment Fab ABD1556, light chain…
- EC
- 2.7.11.30
- UniProt
- P36894
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody fragment Fab ABD1556, heavy chain | protein | 207 | 6% helix, 55% strand | — |
| L, M, N, O | Antibody fragment Fab ABD1556, light chain | protein | 210 | 8% helix, 48% strand | — |
| A, B, C, D | Bone morphogenetic protein receptor type-1A (EC 2.7.11.30) | protein | 85 | 0% helix, 36% strand | P36894 |
| I | Antibody fragment Fab ABD1556, heavy chain | protein | 215 | 7% helix, 53% strand | — |
| J | Antibody fragment Fab ABD1556, heavy chain | protein | 221 | 5% helix, 52% strand | — |
| K | Antibody fragment Fab ABD1556, heavy chain | protein | 215 | 6% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.74 | 0.78 | 77 | empty |
| 2 | 1192 | 0.74 | 0.77 | 66 | empty |
| 3 | 777 | 0.68 | 0.75 | 75 | empty |
| 4 | 460 | 0.68 | 0.79 | 62 | empty |
| 5 | 439 | 0.68 | 0.80 | 59 | empty |
Interfaces
23 interfaces between chains.
- J–N · 1841 Ų buried · 11 hydrogen bonds · protein-protein
- K–O · 1812 Ų buried · 16 hydrogen bonds · protein-protein
- I–M · 1768 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1766 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 883 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 3NH7 · Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I… · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P36894
- Elsewhere: RCSB PDB 3NH7 · PDBe 3NH7 · UniProt P36894
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